The scant number of available metabolomics biomarkers does not reflect the extent of the research in this field. Looking for the reasons of failure, the authors, as analytical chemists, critically discuss each of the steps in the analytical process that requires improvements. They find insufficient information about how the experimental part is developed. After revising the steps from sampling to obtainment of the analytical sample (from typical samples such as blood and urine to others less common such as sweat or saliva), the need for data and metadata for either reproduction of a given study or for taking the study as starting point after biomarker discovery is criticized. The separation and analysis steps are also revised as does data treatment. After the sources of errors from the analytical process are overcome, subsequent steps in the implementation of biomarkers to reach the final aim of clinical adoption should be supported as required.